Patches to add doxygen support to build and add some comments.

[Jef Driesen]

Ryan,

I've always wanted to improve the documentation and generate manuals, 
but never really had (or made) time for it. I quickly checked your 
patches, and have a few comments/questions:

When building outside the source tree (which is my personal default), 
nothing gets documented. So this will need some more improvements.

Is there a reason why you did reformat the existing documentation? I 
prefer the original format with the javadoc style syntax.

You also started to document some internal stuff. But none of that is 
supposed to end up in the documentation! The part that needs to be 
documented are the public header files.

Jef